Sunday, March 01, 2009

Spectral Game update

The end of February 09 has come and gone and nobody hit the 100 points to win the molecular model kit I announced earlier for the Spectral Game. The highest score in that time period was 75.

Since my CHEM242 class is having 2 tests and one exam in the next 3 weeks I thought I would make the next prize available to them exclusively. The student from that class who scores highest by 9:50 Wednesday March 4, 2009 will win a molecular model kit. That happens to be the end of class on that day. The scores have been reset.

The game has been improved considerably during the past few weeks. A few security flaws were fixed, including modifying what metadata can be viewed via JSpecView and preventing the refresh button from selecting a new set of molecules. The game play was also changed to get increasingly more difficult over time, including adding more molecules and a timeout after the first set of ten spectra. This work was a collaboration between Andrew Lang, Antony Williams, Robert Lancashire and myself.

We are very excited by what we have put together so far. There are currently 457 H NMR, 389 C NMR, 11 IR and 29 NIR spectra. This is only possible because of people who submitted their spectra to ChemSpider as Open Data - please keep uploading!

The game has been played 1,824 times, viewing the spectra a total of 8,652 times - with a lot of curation by users. (If you see something wrong with a spectrum you can write a note and that helps us clean up the database). We have had 612 unique visitors from 37 different countries - a total of 13,919 page views in just over two weeks!

We now have a wiki with key links relating to the game. I also added the NMR notes from my CHEM242 class and we'll keep collecting resources. This could become a helpful resource to learn about NMR and practice it by playing the game.

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At 3:16 AM, Blogger Egon Willighagen said...

Nice to hear that this has been so big a success!

Do you have a list of those spectra? Or can I easily query ChemSpider to get a list of structures with your OpenData spectra?

At 9:52 AM, Blogger ChemSpiderman said...

Egon, You can visit and see the list of Open Data spectra.

As one of the advocates of Open Data and one of the biggest contributors of spectra to NMRSHiftDB would you be willing to provide us the spectral curves associated with the spectra you deposit to NMRShiftDB or are these just extracted from the literature and you don't have access to spectral curves?

Would you ask the community to support our efforts via your blog please? Thanks

At 10:02 AM, Blogger Egon Willighagen said...

Antony, my contributions to the NMRShiftDB come mostly from literature, so no access to spectral curves. Otherwise, I would have loved to submit them.

Thanx for the link to spectra.aspx. That HTML combined with JavaScript is not quite a convenient way to download the Open Data, unfortunately :(

My interest in downloading the data would be in finding out which structures with Open Spectra are not found in the NMRShiftDB, and therefore good candidates for annotation.

BTW, many of my NMRShiftDB contributions are actually for uncommon nuclei, that is, not proton, not carbon.

At 1:59 PM, Blogger ChemSpiderman said...

When we have time we will work on a way to download the data in a more facile fashion. Not sure when that will be though as, as usual, there is a long list or priorities ahead of it. The majority of the new data are from Heinz Kolshorn and are the last 15 or so spectra in that list. I love exotic nuclei and have published on N-15, Te-125, Se-77, P-31, Co-59 and worked on many more - Pt, V, B, Xe etc

At 2:50 PM, Blogger Egon Willighagen said...

Oh, feel free to send me a few reprints of papers where you have spectra for a series of compounds. I'm testing the new (Bioclipse2-based) Speclipse client for submitting entries to the NMRShiftDB.

At 3:27 PM, Blogger ChemSpiderman said...

I'll send you a manuscript of N15 shifts and assignments...a couple of hundred structures.

I just left a comment on your would be good to get a web service on NMRShiftDB so that we can call the assignments for a structure by passing an InChI-String, InChIKey or StdInChIs? It would require the InChis layering onto the DB but that would be easy. We could then return the assignments and display in ChemSpider and have the option to display the assignments on the Spectral Game if we do the work to upload the assignments. Possible?

At 1:22 AM, Blogger Egon Willighagen said...

Yes, possible.

You cannot pass it an InChI, I think, but you can search compounds (CML), which will return you a CMLSpect document with all details.

There is also a service that predicts spectra, which is used in Speclipse to returns an educated guess of the assignments.


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